Yet, as those criminals are revealed to have more depth than was at first apparent, the various protagonists are left with disturbing questions: "What exactly is the definition of 'human' in a society where a mind can be copied and the body replaced with a synthetic form?", "What exactly is the 'ghost' —the human soul— in the cybernetic body, or 'shell'?", "Where is the boundary between human and machine when the differences between the two become more philosophical than physical?", etc.

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In Ghost in the Shell, the word "ghost" (ゴースト,gōsuto?) is colloquial slang for an individual's consciousness. In the manga's futuristic society, science has redefined the ghost as the thing that differentiates a human being from a biological robot. Regardless of how much biological material is replaced with electronic or mechanical substitutes, as long as individuals retain their ghost, they retain their humanity and individuality.

The concept of the ghost was borrowed by Masamune Shirow from an essay on structuralism, The Ghost in the Machine, by Arthur Koestler. The title itself was originally used by an Englishphilosopher, Gilbert Ryle, to mock the paradox of conventional Cartesian dualism and dualism in general. Koestler, like Ryle, denies Cartesian dualism and locates the origin of human mind in the physical condition of the brain. He argues that the human brain has grown and built upon earlier, more primitive brain structures, the "ghost in the machine", which at times overpower higher logical functions, and are responsible for hate, anger and other such destructive impulses. Shirow denies dualism similarly in his work, but defines the "ghost" more broadly, not only as a physical trait, but as a phase or phenomenon that appears in a system at a certain level of complexity. The brain itself is only part of the whole neural network; if, for example, an organ is removed from a body, the autonomic nerve of the organ and consequently its "ghost" will vanish unless the stimulus of the existence of the organ is perfectly re-produced by a mechanical substitution. This can be compared, by analogy, to a person born with innate deafness being unable to understand the concept of "hearing" unless taught.

Ghost-dubbing, or duplicating a ghost, is a near-impossible act in the Ghost in the Shell universe. When performed, as a cheap AI substitute in Innocence and earlier in the manga, the result is always inferior to the original-which always dies in the process. In Stand Alone Complex, criminals use a ghost-dubbing device to create numerous duplicates of South American drug lord Marcelo Jarti; after the original died, the device continued to duplicate him into a near-infinite number of bodies with identical memories and personalities, essentially immortalizing him.

In Ghost in the Shell, Kusanagi completely reproduces the stimulus of all of her organs in order to maintain her "ghost". If a technical error arises during the transfer of a "ghost" from one body to another, the transfer normally results in failure, since the "ghost" tends to deteriorate due to either the difference of system at the material level or the deficiency of the transferring protocol. The Puppet Master manages not to deteriorate its "ghost" when merging with Kusanagi because his system is the body of information itself, thereby avoiding a deterioration due to the deficiency at material level.

An important concept within Ghost in the Shell is that evolution is the process of merging two sets of data (DNA) in order to create a third set of data which contains the most vital elements of the original organisms along with some element of chance. The Puppet Master has evolved beyond DNA as a datum set and thus to procreate (his true desire and purpose for leaving the net in the first place) this new organism (a soul not born of DNA) a new paradigm of data merging needs to be contemplated for which he has sought Kusanagi out. This is a merger of two operating "souls" or "ghosts" into one mind, which is specifically different from birth while being simultaneously analogous to it.

Fuchikomas(フチコマ?) and Tachikomas(タチコマ?) are artificially intelligent mini-tanks (walkers) employed by Section 9. Because of the demands of field duty, these robots are constructed with extremely flexible, adaptable AIs that lack many of the safeguards present in other artificially intelligent robots. While this enables them to behave unpredictably and flexibly in the heat of battle, it also presents difficulties for the members of Section 9, who must monitor the Tachikoma closely for signs of undesirable emotional development.

Tachikoma often ask questions that most people would not think of, much like children that are trying to understand the world, yet with superior thinking capabilities. There are Tachikoma short clips that involve them discussing complex philosophical issues and how they relate to existence. They provide more of an innocent look on the world that surrounds them. The Tachikomas are also used to approach the question of whether or not one's individuality can withstand a parallelization of information from a different perspective.

While originally intended to "underscore the dilemmas and concerns that people would face if they relied too heavily on the new communications infrastructure,"[1] Stand Alone Complex (スタンド・アローン・コンプレックス,Sutando Arōn Konpurekkusu?) eventually came to represent a phenomenon where unrelated, yet very similar actions of individuals create a seemingly concerted effort.

A Stand Alone Complex can be compared to the emergentcopycat behavior that often occurs after incidents such as serial murders or terrorist attacks. An incident catches the public's attention and certain types of people "get on the bandwagon", so to speak. It is particularly apparent when the incident appears to be the result of well-known political or religious beliefs, but it can also occur in response to intense media attention. For example, a mere fire, no matter the number of deaths, is just a garden variety tragedy. However, if the right kind of people begin to believe it was arson, caused by deliberate action, the threat that more arsons will be committed increases dramatically.

What separates the Stand Alone Complex from normal copycat behavior is that there is no real originator of the copied action, but merely a rumor or an illusion that supposedly performed the copied action. There may be real people who are labeled as the originator, but in reality, no one started the original behavior. And in Stand Alone Complex, the facade just has to exist in the minds of the public. In other words, a potential copycat just has to believe the copied behavior happened from an originator - when it really did not. The result is an epidemic of copied behavior having a net effect of purpose. One could say that the Stand Alone Complex is mass hysteria over nothing - yet causing an overall change in social structure.

This is not unlike the concepts of memes (refer to the conversation between the major and the Puppet Master in the manga) and second-order simulacra. It also has ties to social theory, as illustrated in the work of Frederic Jameson and Masachi Osawa. The Slender Man phenomenon, in which the fictitious concept of a supernatural murderer went viral and has allegedly inspired real attacks, may be seen as an example of the Stand Alone Complex.

It has been posited that the choice by the writers of Ghost In The Shell: Stand Alone Complex to use J.D. Salinger's short story "The Laughing Man" as a key element in the story was itself an example of second-order simulacra; the use of a story that could already be considered an example of second-order simulacra, by its popularity overshadowing the popularity of its original, The Man Who Laughs. This creates yet another example of the concept, by banking on the popularity of the show, the character, and the emblem used to represent The Laughing Man, supplanting the story as the Laughing Man by popularity alone.

In the series itself, it usually refers to events surrounding the Laughing Man case, and to some extent, the teamwork observed in Public Security Section 9. It is presented as an emergent phenomenon catalyzed by parallelization of the human psyche through the cyberbrain networks.[2] A key point is that due to the electronic communications network that is increasingly permeating society, more and more people are being exposed to the same information and stimuli, making the overall psyche and responses of large groups of people increasingly similar; the result is an exponential increase in the potential for copycat behavior that forms a Stand Alone Complex. There is no original Laughing Man, no leader. Everyone is acting on their own, yet a coherent whole emerges. There are people who employed the copycat behavior before others, but what started the coherent whole is uncertain.

In Ghost in the Shell: S.A.C. 2nd GIG, the Stand Alone Complex theory is expanded to political action. The main antagonist of the series, Goda, attempts to spark a revolution by what he terms "data manipulation" to create the prerequisite conditions for a Stand Alone Complex. By manipulating the fear and frustration of the repressed Chinese refugees in Japanese society, as well as creating false information which is then "leaked" to the police and Public Security Section 9, a terrorist organization calling itself "The Individual Eleven" emerges. However, with each terrorist incident, including an attempt to assassinate the Prime Minister, it becomes clear that nothing connects the incidents together besides a logo, which had been "leaked" by Goda. In other words, "The Individual Eleven" is an organization constructed by a Stand Alone Complex - a group of self-interested individuals who have no connection or ties to each other but who unconsciously and collectively act towards the common purpose of revolution. Goda notes that there is a tendency within a Stand Alone Complex for the masses to unconsciously project their inadequacies and common desires onto a leader. In the first Stand Alone Complex series, this was the Laughing Man, and in Ghost in the Shell: S.A.C. 2nd GIG, this figure is unconsciously realized in the form of Hideo Kuze.